tbuckley/cabot-search huggingface dataset:
Trauma-Informed Ethics Consultation in the ICU: Exploring Best Practices in a Case Involving a Self-Inflicted Gunshot Wound
Authors: Anita J. Tarzian
Journal: The American Journal of Bioethics (2023)

"Trauma-Informed Ethics Consultation in the ICU: Exploring Best Practices in a Case Involving a Self-Inflicted Gunshot Wound." The American Journal of Bioethics, 23(1), pp. 96–97This article is referred to by:Trusting the Ethics Consultant: Adopting a Trauma-Informed Approach to Ethics ConsultationWhose Trauma? Who’s Trauma Informed?“What Does a Life Worth Living Mean to You?” Narrative Approaches to Ethics Consultation in the Context of Trauma, Treatment Refractory Depression, and Life-Sustaining Care Refusals Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells
Authors: Myeong Joon Kim, Kyungsoo Kim, Hyo Jin Park, Gil-Ran Kim, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, Dong Jin Park, Dahae Kim, Je-Min Choi, Insuk Lee, Sang-Jun Ha
Journal: Nature Immunology (2022)
Rethinking the Moral Authority of Experience: Critical Insights and Reflections from Black Women Scholars
Authors: Faith E. Fletcher, Folasade C. Lapite, Alicia Best
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Bioethics and the Moral Authority of Experience Additional informationFundingFaith E. Fletcher's work was supported in part by the National Human Genome Research Institute of the National Institutes of Health under award number K01HG011495-01.
Trusting the Ethics Consultant: Adopting a Trauma-Informed Approach to Ethics Consultation
Authors: L. R. Sankary, G. Morley, P. J. Ford
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Trauma-Informed Ethics Consultation in the ICU: Exploring Best Practices in a Case Involving a Self-Inflicted Gunshot Wound Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Behavior Contracts Are Not Psychologically Naïve
Authors: Michael Redinger
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Response to Open Peer Commentaries on “Ethical Issues in Using Behavior Contracts to Manage the ‘Difficult’ Patient Family”This article refers to:Ethical Issues in Using Behavior Contracts to Manage the “Difficult” Patient and Family Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Paperwork: Put Behavior Contracts at the Bottom of the Pile
Authors: Caroline Ann Buchanan
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Response to Open Peer Commentaries on “Ethical Issues in Using Behavior Contracts to Manage the ‘Difficult’ Patient Family”This article refers to:Ethical Issues in Using Behavior Contracts to Manage the “Difficult” Patient and Family Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Unique Ethical and Practical Considerations in the Use of Behavior Contracts for Families of Minors and Minoritized Populations in Pediatric Settings
Authors: Aleksandra E. Olszewski, Lori Mendelsohn, Erin Talati Paquette
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Response to Open Peer Commentaries on "Ethical Issues in Using Behavior Contracts to Manage the 'Difficult' Patient Family"This article refers to:Ethical Issues in Using Behavior Contracts to Manage the "Difficult" Patient and Family DISCLOSURE STATEMENTNo potential conflict of interest was reported by the author(s).Additional informationFundingDr. Paquette reports funding support under the NIH NICHD L40 HD089260, K12HD047349, and 1K23HD09828901A1, which supported time during which the manuscript was completed.
Disability Bioethics and the “Liabilities” of Personal Experience
Authors: Kevin Todd Mintz
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Bioethics and the Moral Authority of Experience AcknowledgmentsThe author thanks Andy Dogali, Meghan Halley, and Sawyer Skye Lucas-Griffin for helpful comments on previous drafts of this commentary.Additional informationFundingThis work was supported by National Human Genome Research Institute.
Behavior Contracts and Lessons from Parenting “Rotten” Kids
Authors: Jolion McGreevy, Rosamond Rhodes
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Response to Open Peer Commentaries on “Ethical Issues in Using Behavior Contracts to Manage the ‘Difficult’ Patient Family”This article refers to:Ethical Issues in Using Behavior Contracts to Manage the “Difficult” Patient and Family Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Responding to Parental Objections Over Testing for Death by Neurologic Criteria
Authors: Ian D. Wolfe
Journal: The American Journal of Bioethics (2023)

"Responding to Parental Objections Over Testing for Death by Neurologic Criteria." The American Journal of Bioethics, 23(1), pp. 94–95This article refers to:Disputes over Diagnosing Death: Is It Ethical to Test for Death by Neurologic Criteria over Parental Objection? Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Transforming Behavior Contracts Into Collaborative Commitments With Families
Authors: Jerry Schwartz, Dawn Nebrig, Laura Monhollen, Armand H. Matheny Antommaria
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Response to Open Peer Commentaries on "Ethical Issues in Using Behavior Contracts to Manage the 'Difficult' Patient Family"This article refers to:Ethical Issues in Using Behavior Contracts to Manage the "Difficult" Patient and Family Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
Ethics, Engagement, and Escalating Interventions
Authors: John S. Rozel
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article is referred to by:Response to Open Peer Commentaries on "Ethical Issues in Using Behavior Contracts to Manage the 'Difficult' Patient Family"This article refers to:Ethical Issues in Using Behavior Contracts to Manage the "Difficult" Patient and Family Additional informationFundingThe author(s) reported there is no funding associated with the work featured in this article.
What is “Personal” About Personal Experience? A Call to Reflexivity for All
Authors: Colin Halverson, Meghan Halley
Journal: The American Journal of Bioethics (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Bioethics and the Moral Authority of Experience Additional informationFundingCMEH is supported by [grant number K01HG012408], and MCH is supported by [grant number K01HG011341], both from the National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
SHP-2 and PD-1-SHP-2 signaling regulate myeloid cell differentiation and antitumor responses
Authors: Anthos Christofides, Xanthi-Lida Katopodi, Carol Cao, Dimitra Karagkouni, Konstantinos Aliazis, Sasitorn Yenyuwadee, Halil-Ibrahim Aksoylar, Rinku Pal, Mohamed A. A. Mahmoud, Laura Strauss, Natalia M. Tijaro-Ovalle, Louis Boon, John Asara, Ioannis S. Vlachos, Nikolaos Patsoukis, Vassiliki A. Boussiotis
Journal: Nature Immunology (2022)

Abstract The inhibitory receptor PD-1 suppresses T cell activation by recruiting the phosphatase SHP-2. However, mice with a T-cell-specific deletion of SHP-2 do not have improved antitumor immunity. Here we showed that mice with conditional targeting of SHP-2 in myeloid cells, but not in T cells, had diminished tumor growth. RNA sequencing (RNA-seq) followed by gene set enrichment analysis indicated the presence of polymorphonuclear myeloid-derived suppressor cells and tumor-associated macrophages (TAMs) with enriched gene expression profiles of enhanced differentiation, activation and expression of immunostimulatory molecules. In mice with conditional targeting of PD-1 in myeloid cells, which also displayed diminished tumor growth, TAMs had gene expression profiles enriched for myeloid differentiation, activation and leukocyte-mediated immunity displaying &gt;50% overlap with enriched profiles of SHP-2-deficient TAMs. In bone marrow, GM-CSF induced the phosphorylation of PD-1 and recruitment of PD-1-SHP-2 to the GM-CSF receptor. Deletion of SHP-2 or PD-1 enhanced GM-CSF-mediated phosphorylation of the transcription factors HOXA10 and IRF8, which regulate myeloid differentiation and monocytic-moDC lineage commitment, respectively. Thus, SHP-2 and PD-1-SHP-2 signaling restrained myelocyte differentiation resulting in a myeloid landscape that suppressed antitumor immunity.
The phosphatidylinositol-transfer protein Nir3 promotes PI(4,5)P2 replenishment in response to TCR signaling during T cell development and survival
Authors: Wen Lu, Ynes A. Helou, Krishna Shrinivas, Jen Liou, Byron B. Au-Yeung, Arthur Weiss
Journal: Nature Immunology (2022)

Abstract Hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP 2 ) by phospholipase C-γ (PLCγ1) represents a critical step in T cell antigen receptor (TCR) signaling and subsequent thymocyte and T cell responses. PIP 2 replenishment following its depletion in the plasma membrane (PM) is dependent on delivery of its precursor phosphatidylinositol (PI) from the endoplasmic reticulum (ER) to the PM. We show that a PI transfer protein (PITP), Nir3 ( Pitpnm2 ), promotes PIP 2 replenishment following TCR stimulation and is important for T cell development. In Nir3 –/– T lineage cells, the PIP 2 replenishment following TCR stimulation is slower. Nir3 deficiency attenuates calcium mobilization in double-positive (DP) thymocytes in response to weak TCR stimulation. This impaired TCR signaling leads to attenuated thymocyte development at TCRβ selection and positive selection as well as diminished mature T cell fitness in Nir3 –/– mice. This study highlights the importance of PIP 2 replenishment mediated by PITPs at ER-PM junctions during TCR signaling.
Engineering human stem cell-derived islets to evade immune rejection and promote localized immune tolerance
Authors: Dario Gerace, Quan Zhou, Jennifer Hyoje-Ryu Kenty, Adrian Veres, Elad Sintov, Xi Wang, Kyle R. Boulanger, Hongfei Li, Douglas A. Melton
Journal: Cell Reports Medicine (2023)

Immunological protection of transplanted stem cell-derived islet (SC-islet) cells is yet to be achieved without chronic immunosuppression or encapsulation. Existing genetic engineering approaches to produce immune-evasive SC-islet cells have so far shown variable results. Here, we show that targeting human leukocyte antigens (HLAs) and PD-L1 alone does not sufficiently protect SC-islet cells from xenograft (xeno)- or allograft (allo)-rejection. As an addition to these approaches, we genetically engineer SC-islet cells to secrete the cytokines interleukin-10 (IL-10), transforming growth factor β (TGF-β), and modified IL-2 such that they promote a tolerogenic local microenvironment by recruiting regulatory T cells (T
Promising applications of human-derived saliva biomarker testing in clinical diagnostics
Authors: Mengyuan Song, Hao Bai, Ping Zhang, Xuedong Zhou, Binwu Ying
Journal: International Journal of Oral Science (2023)

Abstract Saliva testing is a vital method for clinical applications, for its noninvasive features, richness in substances, and the huge amount. Due to its direct anatomical connection with oral, digestive, and endocrine systems, clinical usage of saliva testing for these diseases is promising. Furthermore, for other diseases that seeming to have no correlations with saliva, such as neurodegenerative diseases and psychological diseases, researchers also reckon saliva informative. Tremendous papers are being produced in this field. Updated summaries of recent literature give newcomers a shortcut to have a grasp of this topic. Here, we focused on recent research about saliva biomarkers that are derived from humans, not from other organisms. The review mostly addresses the proceedings from 2016 to 2022, to shed light on the promising usage of saliva testing in clinical diagnostics. We recap the recent advances following the category of different types of biomarkers, such as intracellular DNA, RNA, proteins and intercellular exosomes, cell-free DNA, to give a comprehensive impression of saliva biomarker testing.
CD8+ T cell-intrinsic IL-6 signaling promotes resistance to anti-PD-L1 immunotherapy
Authors: Mahrukh A. Huseni, Lifen Wang, Joanna E. Klementowicz, Kobe Yuen, Beatrice Breart, Christine Orr, Li-fen Liu, Yijin Li, Vinita Gupta, Congfen Li, Deepali Rishipathak, Jing Peng, Yasin Şenbabaoǧlu, Zora Modrusan, Shilpa Keerthivasan, Shravan Madireddi, Ying-Jiun Chen, Eleanor J. Fraser, Ning Leng, Habib Hamidi, Hartmut Koeppen, James Ziai, Kenji Hashimoto, Marcella Fassò, Patrick Williams, David F. McDermott, Jonathan E. Rosenberg, Thomas Powles, Leisha A. Emens, Priti S. Hegde, Ira Mellman, Shannon J. Turley, Mark S. Wilson, Sanjeev Mariathasan, Luciana Molinero, Mark Merchant, Nathaniel R. West
Journal: Cell Reports Medicine (2023)

Although immune checkpoint inhibitors (ICIs) are established as effective cancer therapies, overcoming therapeutic resistance remains a critical challenge. Here we identify interleukin 6 (IL-6) as a correlate of poor response to atezolizumab (anti-PD-L1) in large clinical trials of advanced kidney, breast, and bladder cancers. In pre-clinical models, combined blockade of PD-L1 and the IL-6 receptor (IL6R) causes synergistic regression of large established tumors and substantially improves anti-tumor CD8+ cytotoxic T lymphocyte (CTL) responses compared with anti-PD-L1 alone. Circulating CTLs from cancer patients with high plasma IL-6 display a repressed functional profile based on single-cell RNA sequencing, and IL-6-STAT3 signaling inhibits classical cytotoxic differentiation of CTLs in vitro. In tumor-bearing mice, CTL-specific IL6R deficiency is sufficient to improve anti-PD-L1 activity. Thus, based on both clinical and experimental evidence, agents targeting IL-6 signaling are plausible partners for combination with ICIs in cancer patients.
Noncanonical DNA structures are drivers of genome evolution
Authors: Kateryna D. Makova, Matthias H. Weissensteiner
Journal: Trends in Genetics (2023)

In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.
Estimating glomerular filtration rate from serum creatinine concentration in children with augmented renal clearance: all formulas are equivocal, but some are more equivocal than others
Authors: Pascal André, Haithem Chtioui, Kim Dao, Laura E. Rothuizen, Ermindo R. Di Paolo, Manuel Diezi, Pierre-Alex Crisinel, François Cachat, Hassib Chehade, Thierry Buclin
Journal: Kidney International (2023)
Challenges and opportunities in interventions for chronic kidney disease of unknown origin (CKDu): report from the International Society of Nephrology Consortium of Collaborators on CKDu
Authors: Brendan Smyth, Jason Glaser, Jaime Butler-Dawson, Nishantha Nanayakkara, David H. Wegman, Shuchi Anand, Adeera Levin, Ben Caplin, Ricardo Correa Rotter, Kai-Uwe Eckardt, Andrew Fire, David Friedman, Chulani Herath, Vivekanand Jha, Eranga Wijewickrama, Chih-Wei Yang, Divya Bajpai, Maria Pippias, Ifeoma Ulasi, Masaomi Nangaku
Journal: Kidney International (2023)
All Staphylococcus aureus bacteraemia-inducing strains can cause infective endocarditis: Results of GWAS and experimental animal studies
Authors: Sylvère Bastien, Severien Meyers, Wilmara Salgado-Pabón, Stefano G. Giulieri, Jean-Phillipe Rasigade, Laurens Liesenborghs, Kyle J. Kinney, Florence Couzon, Patricia Martins-Simoes, Vincent Le Moing, Xavier Duval, Natasha E Holmes, Niels Eske Bruun, Robert Skov, Benjamin P Howden, Vance G. Fowler, Peter Verhamme, Paal Skytt Andersen, Coralie Bouchiat, Karen Moreau, François Vandenesch
Journal: Journal of Infection (2023)

We aimed at determining whether specific S. aureus strains cause infective endocarditis (IE) in the course of Staphylococcus aureus bacteraemia (SAB). A genome-wide association study (GWAS) including 924 S. aureus genomes from IE (274) and non-IE (650) SAB patients from international cohorts was conducted, and a subset of strains was tested with two experimental animal models of IE, one investigating the early step of bacterial adhesion to inflamed mice valves, the second evaluating the local and systemic developmental process of IE on mechanically-damaged rabbit valves. The genetic profile of S. aureus IE and non-IE SAB strains did not differ when considering single nucleotide polymorphisms, coding sequences, and k-mers analysed in GWAS. In the murine inflammation-induced IE model, no difference was observed between IE and non-IE SAB strains both in terms of adhesion to the cardiac valves and in the propensity to cause IE; in the mechanical IE-induced rabbit model, there was no difference between IE and non-IE SAB strains regarding the vegetation size and CFU. All strains of S. aureus isolated from SAB patients must be considered as capable of causing this common and lethal infection once they have accessed the bloodstream.
Acute Response in the Noninfarcted Myocardium Predicts Long-Term Major Adverse Cardiac Events After STEMI
Authors: Mayooran Shanmuganathan, Ambra Masi, Matthew K. Burrage, Rafail A. Kotronias, Alessandra Borlotti, Roberto Scarsini, Abhirup Banerjee, Dimitrios Terentes-Printzios, Qiang Zhang, Evan Hann, Elizabeth Tunnicliffe, Andrew Lucking, Jeremy Langrish, Rajesh Kharbanda, Giovanni Luigi De Maria, Adrian P. Banning, Robin P. Choudhury, Keith M. Channon, Stefan K. Piechnik, Vanessa M. Ferreira
Journal: JACC. Cardiovascular imaging (2022)

Acute ST-segment elevation myocardial infarction (STEMI) has effects on the myocardium beyond the immediate infarcted territory. However, pathophysiologic changes in the noninfarcted myocardium and their prognostic implications remain unclear.The purpose of this study was to evaluate the long-term prognostic value of acute changes in both infarcted and noninfarcted myocardium post-STEMI.Patients with acute STEMI undergoing primary percutaneous coronary intervention underwent evaluation with blood biomarkers and cardiac magnetic resonance (CMR) at 2 days and 6 months, with long-term follow-up for major adverse cardiac events (MACE). A comprehensive CMR protocol included cine, T2-weighted, T2∗, T1-mapping, and late gadolinium enhancement (LGE) imaging. Areas without LGE were defined as noninfarcted myocardium. MACE was a composite of cardiac death, sustained ventricular arrhythmia, and new-onset heart failure.Twenty-two of 219 patients (10%) experienced an MACE at a median of 4 years (IQR: 2.5-6.0 years); 152 patients returned for the 6-month visit. High T1 (>1250 ms) in the noninfarcted myocardium was associated with lower left ventricular ejection fraction (LVEF) (51% ± 8% vs 55% ± 9%; P = 0.002) and higher NT-pro-BNP levels (290 pg/L [IQR: 103-523 pg/L] vs 170 pg/L [IQR: 61-312 pg/L]; P = 0.008) at 6 months and a 2.5-fold (IQR: 1.03-6.20) increased risk of MACE (2.53 [IQR: 1.03-6.22]), compared with patients with normal T1 in the noninfarcted myocardium (P = 0.042). A lower T1 (<1,300 ms) in the infarcted myocardium was associated with increased MACE (3.11 [IQR: 1.19-8.13]; P = 0.020). Both noninfarct and infarct T1 were independent predictors of MACE (both P = 0.001) and significantly improved risk prediction beyond LVEF, infarct size, and microvascular obstruction (C-statistic: 0.67 ± 0.07 vs 0.76 ± 0.06, net-reclassification index: 40% [IQR: 12%-64%]; P = 0.007).The acute responses post-STEMI in both infarcted and noninfarcted myocardium are independent incremental predictors of long-term MACE. These insights may provide new opportunities for treatment and risk stratification in STEMI.
scEMAIL: Universal and Source-Free Annotation Method for scRNA-Seq Data with Novel Cell-Type Perception
Authors: Hui Wan, Liang Chen, Minghua Deng
Journal: Genomics Proteomics & Bioinformatics (2022)

Current cell-type annotation tools for single-cell RNA sequencing (scRNA-seq) data mainly utilize well-annotated source data to help identify cell types in target data. However, on account of privacy preservation, their requirements for raw source data may not always be satisfied. In this case, achieving feature alignment between source and target data explicitly is impossible. Additionally, these methods are barely able to discover the presence of novel cell types. A subjective threshold is often selected by users to detect novel cells. We propose a universal annotation framework for scRNA-seq data called scEMAIL, which automatically detects novel cell types without accessing source data during adaptation. For new cell-type identification, a novel cell-type perception module is designed with three steps. First, an expert ensemble system measures uncertainty of each cell from three complementary aspects. Second, based on this measurement, bimodality tests are applied to detect the presence of new cell types. Third, once assured of their presence, an adaptive threshold via manifold mixup partitions target cells into "known" and "unknown" groups. Model adaptation is then conducted to alleviate the batch effect. We gather multi-order neighborhood messages globally and impose local affinity regularizations on "known" cells. These constraints mitigate wrong classifications of the source model via reliable self-supervised information of neighbors. scEMAIL is accurate and robust under various scenarios in both simulation and real data. It is also flexible to be applied to challenging single-cell ATAC-seq data without loss of superiority. The source code of scEMAIL can be accessed at https://github.com/aster-ww/scEMAIL and https://ngdc.cncb.ac.cn/biocode/tools/BT007335/releases/v1.0.